Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice
Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants’ growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of <...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/11/2206 |
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| author | Lovepreet Singh Rajat Pruthi Sandeep Chapagain Prasanta K. Subudhi |
| author_facet | Lovepreet Singh Rajat Pruthi Sandeep Chapagain Prasanta K. Subudhi |
| author_sort | Lovepreet Singh |
| collection | DOAJ |
| description | Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants’ growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of <i>indica</i> and <i>japonica</i> rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na<sup>+</sup> concentration, shoot Na<sup>+</sup>:K<sup>+</sup> ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, <i>qSNK4</i>, <i>qSNC9</i>, and <i>qSKC10</i>, which co-localized with the earlier reported QTLs, a novel QTL, <i>qSNC7</i>, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice. |
| first_indexed | 2024-03-11T02:59:54Z |
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| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T02:59:54Z |
| publishDate | 2023-06-01 |
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| spelling | doaj.art-a4933a32304b48aa948a86bc8f1a1ac82023-11-18T08:24:48ZengMDPI AGPlants2223-77472023-06-011211220610.3390/plants12112206Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in RiceLovepreet Singh0Rajat Pruthi1Sandeep Chapagain2Prasanta K. Subudhi3School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USASchool of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USASchool of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USASchool of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USAAlkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants’ growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of <i>indica</i> and <i>japonica</i> rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na<sup>+</sup> concentration, shoot Na<sup>+</sup>:K<sup>+</sup> ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, <i>qSNK4</i>, <i>qSNC9</i>, and <i>qSKC10</i>, which co-localized with the earlier reported QTLs, a novel QTL, <i>qSNC7</i>, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice.https://www.mdpi.com/2223-7747/12/11/2206abiotic stressalkalinity tolerancecandidate genesgenome-wide association study<i>Oryza sativa</i>seedling stage |
| spellingShingle | Lovepreet Singh Rajat Pruthi Sandeep Chapagain Prasanta K. Subudhi Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice Plants abiotic stress alkalinity tolerance candidate genes genome-wide association study <i>Oryza sativa</i> seedling stage |
| title | Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice |
| title_full | Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice |
| title_fullStr | Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice |
| title_full_unstemmed | Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice |
| title_short | Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice |
| title_sort | genome wide association study identified candidate genes for alkalinity tolerance in rice |
| topic | abiotic stress alkalinity tolerance candidate genes genome-wide association study <i>Oryza sativa</i> seedling stage |
| url | https://www.mdpi.com/2223-7747/12/11/2206 |
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